[Biopython] SoC project (BioPython and PyCogent)

[Brad Chapman]

Sofia;

> I'm working on an application for the Summer of Code project of
> integrating BioPython and PyCogent. 

Great -- glad to you hear you are interested in the project.

> I've looked through the list
> archives and saw Brad's general advice to other potential SoC
> applicants, but I thought I'd introduce myself and see if there was
> any advice specific to this project.

The overall goal is to provide integration between Biopython and
PyCogent so programmers can benefit from the unique features and
algorithms in each library. This has two general themes:

- Ensuring interoperability between core objects like sequences,
  alignments and phylogenetic trees.
- Using this interoperability to develop analysis workflows that
  utilize functionality from both libraries.

Within this broad scope you are free to orient your proposal to
whatever set of biological questions that interest you. We've tried
to sketch out some ideas we had on the GSoC page as a starting
point.

> I've used BioPython in the past
> and even explored the code a bit. I'm considering working on one or
> more of the bugs in Bugzilla if I can find time, and will work to
> familiarize myself with PyCogent. Are there any other concepts,
> projects, or people I should familiarize myself with (aside from
> what's listed on the ideas page, of course)? 

Proposals are due this Friday, April 9th and normally require a few
rounds of back and forth revisions to get to a competitive level. My
suggestion would be to focus on learning enough of Biopython and
PyCogent to write out a detailed project plan, with a week by week
description of activities and specific goals.

> As you can see from my
> GitHub and Google Code accounts, I've got some experience with open
> source projects, but please do suggest any specific tools or methods
> you think I should try to get up to speed on, as well. 

The open source work is great; definitely include this in your
proposal. A good outline to start with is:

- Project summary -- A short abstract describing what you hope to
  accomplish during the summer, how you plan to go about it, and
  what motivates you to work on the project.

- Personal summary -- Describe your background and how it will help
  you be successful during GSoC. Here is where you can sell yourself
  to all of the mentors ranking the project: why are you a good
  coder? Why is this project useful to use? How will working on the
  summer project encourage you to stay active in the community?

- Project plan -- The detailed week by week description of plans
  mentioned above.

Hope this helps,
Brad